Navigating Files and Directories

SciencesPo Intro To Programming 2024

Florian Oswald and The Software Carpentry

11 October, 2024

Intro

Questions

• How can I move around on my computer?
• How can I see what files and directories I have?
• How can I specify the location of a file or directory on my computer?

Objectives

• Explain the similarities and differences between a file and a directory.
• Translate an absolute path into a relative path and vice versa.
• Construct absolute and relative paths that identify specific files and directories.
• Use options and arguments to change the behaviour of a shell command.
• Demonstrate the use of tab completion and explain its advantages.

The File System

• The file system organizes data into files and directories on your computer.
• let’s start finding out where we are by running the pwd command - present working directory.

$ pwd

with output:

/Users/nelle

Home Directory Variations

• Linux: /home/nelle
• Windows: C:\Documents and Settings\nelle

if pwd does not return your home directory, may need to navigate there first with cd.

Nelle’s Home Directory

Nelle’s file system looks like this:

The file system is made up of a root directory that contains sub-directories titled bin, data, users, and tmp

• / is the root of the system
• all other locations can be reached from there via a path
• path to homedir is from / to directory Users, which contains folder Nelle
• We know exactly where the home is stored by looking at this path.
• Notice that inside a path, / is a separator. (It’s \ on Windows!)

Working with ls

• type ls -F. This adds option F (for full) to the command.
• now you get also
• a trailing / indicates that this is a directory
• @ indicates a link
• * indicates an executable

$ ls -F

Applications/ Documents/    Library/      Music/        Public/
Desktop/      Downloads/    Movies/       Pictures/

question

What kind of objects does Nelle’s home directory contain?

Help

Clear Terminal

• Use the clear command to clear terminal.
• you can use your ↑ and ↓ keys to see previous commands, or just scroll up.

Getting Help

1. pass the --help option to a command:

$ ls --Help

2. Read the manual entry with man (MacOS and Linux only)

man ls 

3. Search internet for unix man ls

More ls Flags

Challenge

You can also use two options at the same time. What does the command ls do when used with the -l option? What about if you use both the -l and the -h option?

Show Solution

Solution

The -l option makes ls use a long listing format, showing not only the file/directory names but also additional information, such as the file size and the time of its last modification. If you use both the -h option and the -l option, this makes the file size ‘human readable’, i.e. displaying something like 5.3K instead of 5369.

More ls Challenges

Listing in Reverse Chronological Order

By default, ls lists the contents of a directory in alphabetical order by name. The command ls -t lists items by time of last change instead of alphabetically. The command ls -r lists the contents of a directory in reverse order. Which file is displayed last when you combine the -t and -r options? Hint: You may need to use the -l option to see the last changed dates.

Show Solution

Solution

The most recently changed file is listed last when using -rt. This can be very useful for finding your most recent edits or checking to see if a new output file was written.

Getting Data

1. Let’s download some data
2. unzip it and and move it to your home directory. (~, not Desktop!)

Exploring More Directories

• ls can search other than only the current directories.
• Let’s see what is on our home:

$ cd    # goes HOME
$ ls -F .

shows for Nelle only the data we just downloaded:

shell-lesson-data/

• We can also look inside that data from where we are:

$ ls -F shell-less-data

exercise-data/  north-pacific-gyre/

• looks intriguing 🧐. Let’s try and go there!

Going into Subdirectories

• cd is for change directory. Moves the shell to a different location in the file system.
• Let’s go to our data folder:

$ cd shell-lesson-data 
$ cd exercise-data

• Notice that the cd command does not print any output by default.
• Run ls -F again to see what’s in this directory!
• Run pwd to see where we are!

Coming Back from Subdirectories

• Now we want to go back up one level.
• It’s tempting to say cd shell-lesson-data
• But cd can only go into its own subdirectories.
• It has a special one: .. is its parent directory, so goes one up.

$ cd ..
$ pwd

puts Nelle back into

/Users/nelle/shell-lesson-data

• Notice how .. is listed if you flag -a on the ls command.

Hidden Files

Hidden Files

• Typing cd without any arguments puts you back into your Home directory. Do it.
• Let’s use ls -F -a or ls -Fa to list all files. Also hidden ones!

Relative and Absolute Paths

• Up until now, we used relative paths. cd and ls operated from our current position in the file sytem.
• We can also specify the absolute path, i.e. starting at the root /. This allows to go anywhere from anywhere.

More Shortcuts

Tilde (~) and dash (-)

• The tilde ~ in first position means current user’s home
• The dash in cd - means go into the directory I was previously in.
• So:

1. cd .. brings you up one level
2. cd - takes you back to wherever you’ve come from.

Challenges

Challenge

Starting from /Users/amanda/data, which of the following commands could Amanda use to navigate to her home directory, which is /Users/amanda?

1. cd .
2. cd /
3. cd /home/amanda
4. cd ../..
5. cd ~
6. cd home
7. cd ~/data/..
8. cd
9. cd ..

Solution

Show Solution

Solution

1. No: . stands for the current directory.
2. No: / stands for the root directory.
3. No: Amanda’s home directory is /Users/amanda.
4. No: this command goes up two levels, i.e. ends in /Users.
5. Yes: ~ stands for the user’s home directory, in this case /Users/amanda.
6. No: this command would navigate into a directory home in the current directory if it exists.
7. Yes: unnecessarily complicated, but correct.
8. Yes: shortcut to go back to the user’s home directory.
9. Yes: goes up one level.

Challenge

Using the filesystem diagram , if pwd displays /Users/thing, what will ls -F ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original/ pnas_final/ pnas_sub/

Solution

Show Solution

Solution

1. No: there is a directory backup in /Users.
2. No: this is the content of Users/thing/backup, but with .., we asked for one level further up.
3. No: see previous explanation.
4. Yes: ../backup/ refers to /Users/backup/.

Challenge

Using the filesystem diagram below, if pwd displays /Users/backup,and -r tells ls to display things in reverse order, what command(s) will result in the following output:

pnas_sub/ pnas_final/ original/

is it:

1. ls pwd?
2. ls -r -F?
3. ls -r -F /Users/backup?

Solution

Show Solution

Solution

1. No: pwd is not the name of a directory.
2. Yes: ls without directory argument lists files and directories in the current directory.
3. Yes: uses the absolute path explicitly.

General Syntax of Shell Commands

Let’s take as example this command:

$ ls -F /

General syntax of a shell command

• The space between ls and whatever options you put is important.
• Capitalization is important. ls -s is not the same as ls -S:

$ cd ~/shell-lesson-data
$ ls -s exercise-data  # size
$ ls -S exercise-data  # sort by size

Nelle’s Pipeline and Tab Completion

1. Nelle organized the output of the assay machine into north-pacific-gyre/. let’s go there.

$ cd ~/shell-lesson-data/
$ cd north-pacific-gyre

2. Now north-pacific-gyre is a mouthful to write. try instead to type cd n and hit the TAB key.
3. hitting TAB twice without any leading character, gives you a list of files in pwd.

Key Points

• The file system is responsible for managing information on the disk.
• Information is stored in files, which are stored in directories (folders).
• Directories can also store other directories, which then form a directory tree.
• pwd prints the user’s current working directory.
• ls [path] prints a listing of a specific file or directory; ls on its own lists the current working directory.
• cd [path] changes the current working directory.
• Most commands take options that begin with a single -.
• Directory names in a path are separated with / on Unix, but \\ on Windows.
• / on its own is the root directory of the whole file system.
• An absolute path specifies a location from the root of the file system.
• A relative path specifies a location starting from the current location.
• . on its own means ‘the current directory’; .. means ‘the directory above the current one’.